Variant report

Variant	rs3824492
Chromosome Location	chr9:98685797-98685798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98637678..98640109-chr9:98685155..98688009,2	K562	blood:
2	chr9:98665770..98668209-chr9:98683792..98686437,2	K562	blood:
3	chr9:98636162..98639165-chr9:98683503..98686735,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000199202	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11794391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12684321	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359916	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910257	0.88[GIH][hapmap]
rs3088294	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60399336	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62562984	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs963150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv1801890	chr9:98660433-98701801	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3824492	NCBP1	cis	cerebellum	SCAN
rs3824492	C9orf102	cis	cerebellum	SCAN
rs3824492	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
2	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:98644600-98690800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:98645800-98702200	Weak transcription	Aorta	Aorta
5	chr9:98649400-98694400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
7	chr9:98660000-98706000	Weak transcription	Fetal Heart	heart
8	chr9:98664000-98687400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:98670800-98687200	Weak transcription	Stomach Mucosa	stomach
10	chr9:98673600-98702200	Weak transcription	Small Intestine	intestine
11	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
12	chr9:98676600-98693200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr9:98677200-98686200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:98677200-98688400	Strong transcription	A549	lung
15	chr9:98677400-98688400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr9:98677400-98688400	Strong transcription	Fetal Muscle Leg	muscle
17	chr9:98677400-98688800	Strong transcription	Dnd41	blood
18	chr9:98677600-98689000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr9:98677600-98709000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr9:98677800-98686600	Strong transcription	Fetal Thymus	thymus
21	chr9:98677800-98687600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:98677800-98688800	Strong transcription	Adipose Nuclei	Adipose
23	chr9:98678000-98686200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:98678000-98688400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr9:98678000-98699200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:98678000-98699600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:98678200-98686200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:98678200-98689200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:98678400-98688400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:98678400-98688800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:98678600-98705600	Weak transcription	Psoas Muscle	Psoas
32	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:98679400-98687400	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:98679400-98695200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:98679400-98698600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:98680600-98686200	Strong transcription	Osteobl	bone
37	chr9:98680800-98706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr9:98681000-98686000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr9:98681400-98685800	Weak transcription	Fetal Intestine Small	intestine
40	chr9:98681400-98690200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr9:98681800-98694400	Weak transcription	Fetal Stomach	stomach
42	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
43	chr9:98682000-98688000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr9:98682000-98688800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:98682200-98685800	Weak transcription	Placenta	Placenta
46	chr9:98682200-98686000	Weak transcription	Ovary	ovary
47	chr9:98682200-98687400	Weak transcription	HSMMtube	muscle
48	chr9:98682400-98698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr9:98682600-98689000	Strong transcription	Fetal Kidney	kidney
50	chr9:98682800-98685800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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